I ran into this problem on 12.04.2 when using 'rtcwake' through cron to put the file server to sleep when nobody is around or everyone is sleeping and having it automatically wake up right before people get home from work or early in the morning on weekends. Whenever the computer wakes up from suspend, the screen randomly flickers, generally more when scrolling.
The 'sleep.sh' command doesn't seem to have this problem. Taking these 5 lines from sleep.sh and adding them to my script right before I call 'rtcwake' seems to solve the problem.
I haven't tried to reverse engineer what those 5 lines do yet, but the solution seems to lie in there. Each of those files it's executing seem to contain various functions that get called through the "DeviceConfig" function, and so one of those functions must do something to the display to cause this problem not to show up.